RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17633
(99 letters)
>gnl|CDD|216184 pfam00907, T-box, T-box. The T-box encodes a 180 amino acid domain
that binds to DNA. Genes encoding T-box proteins are
found in a wide range of animals, but not in other
kingdoms such as plants. Family members are all thought
to bind to the DNA consensus sequence TCACACCT. they are
found exclusively in the nucleus, and perform
DNA-binding and transcriptional activation/repression
roles. They are generally required for development of
the specific tissues they are expressed in, and
mutations in T-box genes are implicated in human
conditions such as DiGeorge syndrome and X-linked cleft
palate, which feature malformations.
Length = 182
Score = 152 bits (386), Expect = 9e-49
Identities = 54/91 (59%), Positives = 69/91 (75%), Gaps = 2/91 (2%)
Query: 9 RMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHP 68
RMFPTL+VS +GL P+ Y+VL+D VPVD+ RY++ H W+VAGKA+P P R+Y+HP
Sbjct: 28 RMFPTLKVSVSGLDPNALYSVLLDFVPVDDHRYKF--HNGEWVVAGKAEPHPPPRVYIHP 85
Query: 69 DSPFTGDQLRKQVVSFEKVKLTNNEMDKNGQ 99
DSP TG KQ VSF+KVKLTNN++D NG
Sbjct: 86 DSPATGAHWMKQPVSFDKVKLTNNKLDGNGH 116
>gnl|CDD|238106 cd00182, TBOX, T-box DNA binding domain of the T-box family of
transcriptional regulators. The T-box family is an
ancient group that appears to play a critical role in
development in all animal species. These genes were
uncovered on the basis of similarity to the DNA binding
domain of murine Brachyury (T) gene product, the
defining feature of the family. Common features shared
by T-box family members are DNA-binding and
transcriptional regulatory activity, a role in
development and conserved expression patterns, most of
the known genes in all species being expressed in
mesoderm or mesoderm precursors.
Length = 188
Score = 151 bits (383), Expect = 3e-48
Identities = 52/91 (57%), Positives = 68/91 (74%), Gaps = 2/91 (2%)
Query: 9 RMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHP 68
RMFPTL+V +GL P+ Y+VLMD+VPVD+ RY+++ W+VAGKA+P P R+Y+HP
Sbjct: 30 RMFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFSG--GKWVVAGKAEPHLPPRVYVHP 87
Query: 69 DSPFTGDQLRKQVVSFEKVKLTNNEMDKNGQ 99
DSP TG KQ VSF+K+KLTNN +D NG
Sbjct: 88 DSPATGAHWMKQPVSFDKLKLTNNTLDNNGH 118
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 138 bits (351), Expect = 2e-43
Identities = 54/90 (60%), Positives = 69/90 (76%), Gaps = 2/90 (2%)
Query: 9 RMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHP 68
RMFPTL+ +GL P+ Y+VLMD+VPVD+KRY++ + W+VAGKA+P P R+Y+HP
Sbjct: 29 RMFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKF--NNGKWVVAGKAEPHMPSRVYVHP 86
Query: 69 DSPFTGDQLRKQVVSFEKVKLTNNEMDKNG 98
DSP TG KQ VSF+KVKLTNN+ DKNG
Sbjct: 87 DSPATGAHWMKQPVSFDKVKLTNNQSDKNG 116
>gnl|CDD|233774 TIGR02195, heptsyl_trn_II, lipopolysaccharide heptosyltransferase
II. This family consists of examples of ADP-heptose:LPS
heptosyltransferase II, an enzyme of LPS inner core
region biosynthesis. LPS, composed of lipid A, a core
region, and O antigen, is found in the outer membrane of
Gram-negative bacteria [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 334
Score = 33.9 bits (78), Expect = 0.007
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 19 TGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADP-PAPLRL 64
TG R + RY +L D+ +D +R R L K P PL
Sbjct: 105 TGWRGEMRYGLLNDVRALDKERLPLMVERYIALAYDKGQDLPQPLPR 151
>gnl|CDD|204133 pfam09101, Exotox-A_bind, Exotoxin A binding. Members of this
family are found in Pseudomonas aeruginosa exotoxin A,
and are responsible for binding of the toxin to the
alpha-2-macroglobulin receptor, with subsequent
internalisation into endosomes. The domain adopts a
thirteen-strand antiparallel beta jelly roll topology,
which belongs to the Concanavalin A-like
lectins/glucanases fold superfamily.
Length = 274
Score = 31.6 bits (71), Expect = 0.043
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 11 FPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSS-------WLVAGKADPPAPLR 63
F T+R + D + V+ + +N RY+Y+R + WLV D PA ++
Sbjct: 73 FATIRAEGHYVNQDAPFGVIHLDITEENGPKRYSYNRKAEGEFAINWLVPIGEDKPANIK 132
Query: 64 LYMH 67
+++
Sbjct: 133 IFID 136
>gnl|CDD|215974 pfam00529, HlyD, HlyD family secretion protein.
Length = 304
Score = 27.8 bits (62), Expect = 0.83
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 21 LRPDQRYAV---LMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRLYMHPDSPFT 73
++ + V LM +VP N A + L + P APL ++ T
Sbjct: 188 VQVGEEVGVGSPLMGVVP-FNDVEVDANLGETQLRLVRPGPRAPLTGGVYVLVVLT 242
>gnl|CDD|227881 COG5594, COG5594, Uncharacterized integral membrane protein
[Function unknown].
Length = 827
Score = 27.4 bits (61), Expect = 1.3
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 4 LSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVP 35
L L+ P L TGL P ++LM IVP
Sbjct: 450 LKFILKDPPFLAGILTGLLPTVALSLLMSIVP 481
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 26.8 bits (59), Expect = 2.3
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 22 RPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKADPPAPLRL-------YMHPDSPF 72
R +R V ++I+ + ++ R WL AGK P AP RL Y D+P+
Sbjct: 422 RTLERCGVKVEILGFTTRAWKGGQSREKWLKAGK--PAAPGRLNDLRHIIYKSADAPW 477
>gnl|CDD|221098 pfam11376, DUF3179, Protein of unknown function (DUF3179). This
family of proteins has no known function.
Length = 261
Score = 26.1 bits (58), Expect = 3.3
Identities = 9/39 (23%), Positives = 12/39 (30%)
Query: 18 FTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWLVAGKA 56
F PD R ++ VD A+ AG
Sbjct: 174 FPVGHPDDRLPPKERVLGVDTGGGAVAFPLDELRAAGVI 212
>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740). This
family consists of several uncharacterized plant
proteins of unknown function.
Length = 565
Score = 26.1 bits (57), Expect = 3.6
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 24 DQRYAVLMDIVPVDNKRYRYAYHRSSW----LVAGKADPPAPLRLYMHPDSPFTGDQLRK 79
D R+++ + VD+ RY + R+SW + A PP P L + D+P +
Sbjct: 246 DPRFSLDAGRISVDDPRYSFDEPRASWDGCLIGRTYAPPPLPSMLSVVEDAPVERSDM-- 303
Query: 80 QVVSFEKVKLTNNEMD 95
Q+ V+ E D
Sbjct: 304 QIPVEPSVEEEEVEED 319
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 25.9 bits (56), Expect = 4.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 33 IVPVDNKRYRYAYHRSSWLV 52
IVP D R R+A R+ W V
Sbjct: 13 IVPFDESRIRWAVQRAMWEV 32
>gnl|CDD|220234 pfam09423, PhoD, PhoD-like phosphatase.
Length = 452
Score = 25.6 bits (57), Expect = 5.1
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 13 TLRVSFTGLRPDQRY 27
T++V TGL P +RY
Sbjct: 63 TVKVDVTGLPPGRRY 77
>gnl|CDD|187832 cd09701, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
inactivated palm domain and Zn-ribbon; signature gene
for type III.
Length = 909
Score = 25.5 bits (56), Expect = 6.5
Identities = 6/38 (15%), Positives = 12/38 (31%)
Query: 14 LRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWL 51
L + ++ ++R L K R+ S
Sbjct: 718 LEKTKKLVQVNRRSVPLFWAQSYSTKDKRWLDLWSPLK 755
>gnl|CDD|170049 PRK09692, PRK09692, integrase; Provisional.
Length = 413
Score = 25.4 bits (55), Expect = 7.2
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 4 LSHFLRMFPTLRVSFTGLRPDQRYAVLMDIVPVDNKRYRYAYHRSSWL 51
+SH LR + ++ G PD A L VD R AY+RS +L
Sbjct: 335 VSHGLRSIASTALNEQGFPPDVIEAALAH---VDKNEVRRAYNRSDYL 379
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.138 0.422
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,286,106
Number of extensions: 443982
Number of successful extensions: 364
Number of sequences better than 10.0: 1
Number of HSP's gapped: 361
Number of HSP's successfully gapped: 18
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)